The eradication of psychedellic and psycho active plants, as well as being a means of forcing indigenous people off their lands in order to exploit the wealth beneath the ground, is a means of sabotaging the culture and world view that indigenous cultures offer and which directly challenges the foundations of what Leslie Marmon Silko calls "The Destroyer" culture in her novel The Almanac of the Dead.  (In this 1991 novel Silko speaks of a sort of spiritual brotherhood between Montezuma and the conquistadors and of an indigenous movement, starting in Chiapas, to reclaim the continent from the destoyers.)

There are strong parallels through the modern cultural genocide(1) against the indigenous peoples of the Andes and the historical repression of witches, herbalists, and midwives in Europe.  In her new book, The Earth Path(San Francisco: Harper Collins, 2004,)Starhawk writes:

"In the sixteenth and seventeenth centuries, there were still areas of common land in Europe that belonged to the community rather than individuals.  While land ownership was highly concentrated and enormously hierarchical, land was nevertheless not considered mere property that could be bought or sold in isolation -- but rather a nexus of rights and responsibilites deeply tied to a community.  Peasants mught not on any land, but the might have the hereditary right to gather wood in the lord's forest or graze their pigs under his oak trees.  The folk customs -- the maypoles and Morris dances and fairy tales tied to particular places on the landacape -- all reinforeced those traditions. [ . . . ] The view of the land as animated by spirits and nonhuman intelligences was a deterrent to its wholesale exploitation."

An analagous situation exists in Colombia where indigenous and Afro-Colombian have the Constitutional right to live on their ancestral lands.  

"The animat worldview and the way of life it represented were targetd by the Witch persecutions, which had several key impacts. First, they broke some of those ties to the land and attacked the underlying worldview by labelling all traffic with and attunement to those other voices as devil worship.  They helped pave the way for the enclosude of the commons, the privatization of what had once been collectively held -- a process which continues on today through global trade agreeements and development.  They also undermined the solidarity of the peasant class, which ahd mounted a series of rebellions over the centuries."

Today the criminalization of the cultivation and use of sacred psychoactive plants undermines a worldview that sees the Earth as alive and these plants as a means of experiencing that connection, undermines the solidarity of indigenous communities, criminalizes indigenous peole, and serves as a pretext for forcing indigenous people off collectively held land.

"Second, they were an attack on forms of knowledge and healing that did not have the approval of the authorities. Midwives, herbalists, and traditional healers, many of whom were women, were considered suspect, and the practice of medicine became a specialized activity concentrated in the hands of mail doctors. Although the herbalists of that time were more empirical and truly 'scientific' than the doctors of the day {who were busy bleeding people according to their astrological signs), the doctors' knowledge was considered official and valid while the midwives' and herbalists' knowledge was seen as supersitious of outright traffic with the devil."

The assault on traditional medicine through the criminalization of psychoactive plants renders people dependend on government and corporations for healing, forcing them into a cash economy.

"Finally, they were an attack on women.  Most of the victims were women, and the evils of satanic worship that the Church claimed to find were directly attributed to the generally evil nature of women.  This justified increased represssion and restriction of women's roles."

While there are gender related aspects of the current war on indigeous people in the Andes, today's repression and demonization falls more along racial lines.  
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1) Under international law cultural genocide is defined as actions that consciously destroy or undermine the foundations of a culture -- ie. forced relocation from sacred lands.  As far as I know it is the only internationally defined crime agains the spirit, because the violence it describes is focused primarily on eradicating a culture and a worldview, its physical consequences being merely secondary.